Closed gregcaporaso closed 10 years ago
I'm concerned about bipy.core.sequence.DNA().rc()
, shouldn't this be a classmethod?
yes, probably. can you add an issue to the bipy issue tracker.
On Fri, Jan 31, 2014 at 8:48 AM, Daniel McDonald notifications@github.comwrote:
I'm concerned about bipy.core.sequence.DNA().rc(), shouldn't this be a classmethod?
Reply to this email directly or view it on GitHubhttps://github.com/qiime/qiime/issues/1369#issuecomment-33804975 .
Done, see biocore/bipy#73
cogent.util.misc.app_path
should be replaced with bipy.util.which
(this depends on https://github.com/biocore/bipy/issues/45 being completed first)qiime.util.DistanceMatrix
should be replaced with bipy.core.distance.DistanceMatrix
(see #829). Also, the usage of (sample_ids, data)
distance matrix tuple should be replaced with the new DistanceMatrix
class.this has been split into individual issues, many of which have already been taken care of.
Add to this check list as you identify code that is ready to be changed.
cogent.DNA.rc()
should be replaced with calls to bipy.core.sequence.DNA().rc()``cogent.parse.fasta.MinimalFastaParser
should be replaced with calls tobipy.parse.fasta.MinimalFastaParser
(and we may want to change that name to something likeFastaRecords
as it's a generator of(seq_id, seq)
pairs.